Under the Radar – Diana Crowhttp://dianacrowscience.com
Confessions of a Fledgling Science JournalistTue, 09 Apr 2019 19:41:18 +0000en-UShourly1https://wordpress.org/?v=4.9.10643905927 Things To Know About Mitochondria: 2016 editionhttp://dianacrowscience.com/7-mitochondria-2016-edition/
http://dianacrowscience.com/7-mitochondria-2016-edition/#commentsFri, 18 Nov 2016 01:50:06 +0000http://dianacrowscience.com/?p=756Mitochondria: To most people, they’re little more than a ghostly memory fragment from middle school biology. However, these tiny “powerhouse(s) of the cell” are much more than they seem.

They’re actually the shape-shifting descendants of ancient bacteria that were eaten by a larger archaebacterium billions of years ago. . (If you want to know more about that theory, check out my recent Lateral magazine piece on the scientist who developed that theory.) Mitochondria have complex relationships with other organelles, swim around in our neurons, and make up 1/3rd of the mass of heart cells. In the past year, scientists have learned how to add and remove them with cellular surgeries and how to manipulate them directly.

Mitochondria live in every cell in your body and are essential for human life. As University of California post doc Samantha Lewis pointed out to me: “There’s mitochondrial involvement in almost every disease.”

Yet, we rarely hear of or think about our cells’ powerhouses.

Here are seven facts you probably haven’t heard about mitochondria:

1: Mitochondria are interconnected shape-shifters.

We say “Mitochondria is the powerhouse of the cell” as if mitochondria is a singular word, but actually it’s plural. (The singular of mitochondria is mitochondrion.) However, in most cells mitochondria act as a collective, passing electrons and genetic information from mitochondrion to mitochondrion.

“They’re [descended from] bacteria that divide in a binary fashion,” explained UC Davis cell biologist and mitochondria specialist Jodi Nunnari. “During the course of evolution [the mitochondrial] genome has been greatly reduced. As a consequence of that and the fact that they were reproducing in a new environment, a few of those do mitochondrial fusion.” Mitochondria’s habit of merging sets them apart from all known bacteria. “Bacteria divide, but they don’t fuse,” Nunnari added.

In fact, mitochondria are so tightly connected that many scientists think of them as a membrane network rather than a series of jelly-bean shaped organelles.

2: Scientists have recently learned how to kinda control their shape-shifting.

Until recently, mitochondrial motives for fusing and dividing have remained murky. However, one team of scientists at Washington University at St. Louis have discovered one molecule that exerts an outsize influence on mitochondrial fusion.

“They have kind of a mob mentality,” Gerald Dorn, a cardiologist from Washington University in St. Louis said of mitochondria. “They do a lot of things that are out of our control.”

However, Dorn and his team recently identified a peptide that is mounted on the ends of individual mitochondria, which opens and closes “like a diaper pin”.

When the diaper pin peptide is “open”, mitochondria stick to each other like Velcro and fuse. When the diaper pin peptide is closed, the mitochondria go on their solitary way.

By adding drugs that open or close the peptide, Dorn and his colleagues were able to mostly control the rate of mitochondrial fusion in the cell. For cell biologists, that’s a new one. The study ran in the prestigious journal Nature.They’re hopeful that someday, the ability to manipulate mitochondrial merging and dividing will lead to treatments for killers like heart disease.

3: They swap genes amongst themselves.

The cell’s nucleus is a hub of genetic information, but mitochondria have kept a handful of their essential genes all to themselves.

Mitochondria store their genetic info on little globs of DNA called nucleoids, which are spread throughout the cell’s mitochondria. Although nucleoids have their own name, they can be thought of as chromosomes for mitochondria. “I do call them mitochondrial chromosomes,” Nunnari admitted.

Nucleoids get shuttled from one mitochondrial compartment to another, and only a small fraction of them are copied to make new mitochondria.

4: Mitochondria are BFFs with the Endoplasmic Reticulum.

[An artist’s rendition of a macrophage with an endoplasmic reticulum by Liz Hirst. Photo by NIMR London via Flickr & CC 2.0 license.]

Samantha Lewis, a postdoc in Nunnari’s lab, recently captured images of strategic bonding between two of cells’ oldest organelles–the powerhouse mitochondria and the molecule-delivering endoplasmic reticulum.

5: Our cells’ powerhouses have their own agenda.

Many biologists tend to forget that mitochondria have their own evolutionary goals, says Maulik Patel of Vanderbilt University. “They retain their own genes and they retain their own genetic interests, and over time, those genetic interests may not necessarily be aligned with the host’s,” he explained.

Because they’re matrilineal, harmful mutations in males don’t make much difference to a mitochondrion’s genetic legacy, Patel says. As long as the females are in good shape, the mitochondrial genome will still get passed to offspring.

“From the perspective of a mitochondrial genome, my sister is much more valuable than I am,” Patel said.

Patel’s lab found evidence of this pheonomenon in action in fruit flies, where they found a mitochondrial mutation that hurts male fertility . They published the study in eLife.

Cells have mitochondrial population control tools to stop the powerhouses from completely overrunning the cytoplasm. However, the mutant mitochondrial strain that Patel and his colleagues studied somehow dodges the population control system.

What happens next mirrors the spread of cancer cells within a body. The mutants divide and divide, overwhelming the host’s quality control mechanisms. The difference is that in this case, the drama happens between organelles within a single yeast cell.

7: We can move them with cellular surgery tools.

In May, researchers debuted a device that can cut into cell membranes with a tiny laser blade. The device burns into the cell membrane with a laser, says study co-author Michael Teitell of UCLA cuts open a small flap of the cell’s outer membrane, a puncture small enough that the cell membrane can heal itself afterwards.

The team then took their experiment a step further by injecting foreign mitochondria into the cell though a tiny glass tube.

Adding healthy mitochondria to sickly cells’ cytoplasm was enough to restore the sick cells’ overall metabolism, the team reported.

Cellular surgeries and biopsies may soon become a regular thing in cell biology. Several other groups are developing similar techniques for physically targeting and transferring microscopic cell parts.

tl;dr:

The lives of our cells’ powerhouses are more complicated than you might think.

Under the Radar: A series of listicles about biology concepts you definitely won’t find in newspaper headlines.

#1: Be a Navigation App for Immune Cells

Natural killer cells, or “NK cells” are the human body’s best defense against cancer. While other types of immune cells often ignore tumor cells, natural killer cells specialize in finding and destroying human cells that look either infected or like cancer mutants. In leukemia patients, a higher number of active natural killer cells ups the patient’s chances for survival, so much so that researchers are experimenting with transfusing NK cells into patients.

Just one problem there: Active natural killer cells die without a strong support network.

KLF2, oddly enough, also exerts a strong navigational influence on the immune system’s T-cells and B-cells. Even though all three types of cells fall under the “white blood cell” umbrella,the notion that one protein could control navigation in all three is pretty weird. Crawling and navigating are complex tasks, requiring coordination between dozens of genes. “[NK cell migration] is totally different from how t-cells and b-cells circulate,” Sebzda said.

Additionally, taking away KLF2 has distinctive effects on each type of cell: KLF2-less t-cells vacate the central body and crawl out to lab mice’s fingers and toes, KLF2-less b-cells all congregate at the spleen (which creates some serious problems for those lab mice), and KLF2-less natural killers end up dying alone.

So KLF2 could be super-useful for improving cancer immunotherapy. But why is KLF2 so versatile in the first place?

The answer lies in KLF2’s ability to bind to a certain recurring DNA base pair sequence, one that presumably earmarks the genes needed in each immune system navigation system, and it’s far from the only protein with such abilities…

Meet the Bogeys: Transcription Factors

If a genome is like a text, it’s one that can be read in many different ways. Every gene serves as a template for a piece of cell machinery, but thousands of biochemicals that play a role in telling the cell which gene template to use when and how many copies to make.

Some of those gene-controlling molecules are based on gene templates themselves. First and foremost among the “meta-genes” are the transcription factors, like KLF2, each of which can land on its own DNA pattern.

The sequences each transcription factor can land on are pretty short. A 9-base-pair sequence like”CATGATTAT” would recur many, many times within a 3-billion-base-pair-containing human genome, so a “CATGATTAT-seeking transcription factor would be able to land on any exposed “CATGATTAT” and influence the expression of nearby genes. (Some TFs boost gene expression; others block it.)

Transcription factors, like alternative splicing, are one of the built-in “hacks” that biology uses to control its traits. (And,as such, are part of a growing field called epigenetics.) Transcription factors (or “TFs“) are particularly adept at switching several different genes on and off in one fell swoop.

(I always kind of imagine transcription factors as being kind of like the Rings of Power in Lord of the Rings. All genes have some power, but like The One Ring, transcription factors have the power to manipulate the other genes. Also, being a transcription-factor specialist renders most of the TF scientists pretty much invisible in science news media….Key difference: There is no one transcription factor gene “to rule them all”. It’s more like a couple thousand TFs to each rule a whole bunch of genes. Unfortunately, that’s less punchy.)

Here are just a few things transcription factors can do:

#2: Tell Neurons Where to Grow

Have you ever wondered how your body makes sure all of the neurons that control your thumbs, forefingers, and toes are wired up correctly?

Every individual motor neuron follows a unique route from the spinal cord to the muscle fiber it controls. (For the neurons in your feet, that means threading a four-and-a-half-foot-long nerve fiber from the base of your spinal cord to the soles of your feet.) Neuroscientists have long been puzzled about how genetically identical proto-motor-neurons manage to navigate budding embryonic limbs.

When they altered the transcription factor codes in mutant fly embryos, the neurons connected to different muscle fibers in the legs. (Flies with the mis-connected neuron weave from side-to-side when they run. The mutant flies, which were otherwise healthy, could walk in straight lines; they just couldn’t run without weaving and zig-zagging all over the place.)

Enriquez and posse concluded that the transcription factor codes are kind of like a combination lock; nascent neurons need to receive three or four different transcription factors in a specific order before they know whether they connect to the kneecap or the pinky toe.

#3: Make an Ordinary Bee a Queen

Some bees live in colonies with a queen-– a lone female who produces all of the eggs on the colony’s behalf– and hundreds or thousands of worker bee sisters who support her but cannot reproduce. Other bees lead a more typical lifestyle, with no queens and no workers, just bees.

The weird thing is: The Queen Bee System– eusociality in technical parlance– has evolved more than once. It’s a complicated change. Worker bees cannot reproduce (except for rare circumstances where the queen gets killed or dies), so the transition from solitary bee-hood to queenly hivedom would have to happen pretty quickly or else, the bee species would be wiped out.

“There have been a lot of success stories in assessing fitness [of eusocial species] from a behavioral ecology standpoint, and most of them have sort of ‘black-boxed’ the mechanisms,” said biologist/bee specialist Karen Kapheim of Utah State University.

A study by Kapheim and her colleagues revealed that the contents of the “black box” of bee social structure vary widely depending on the bee. Kapheim and her colleagues analyzed genomes from ten bee species and found that each of the eusocial groups used a different set of genes to decide who is queen.

But guess what all of the Queen-making mechanisms have in common….Yup. Transcription factors.

The differences between queen bees and their worker daughters and sisters aren’t in DNA base pairs; they’re in the transcription factors that decide when certain genes get expressed. For female bees, at least, there truly are a handful of (transcription-factor-coding) genes that rule them all.

[Update 5/18/16: Kapheim sent me an email saying, “I also would de-emphasize the role of different genes/ TFs in “deciding who is queen”, but rather that these seem to be involved in the overall social patterns of the species.”…Which is an excellent point. I plead “hazard of writing listicle headlines.”]

#4: Broker peace between self-attacking T-cells and bystander cells

Autoimmune diseases suck. They’re subtly-disabling, difficult to diagnose, and even harder to treat. (Plus, they’re on the rise.)

Fortunately, our immune systems have tiny voices of reason called regulatory T-cells or “T-regs”. They patrol our bloodstreams, doing their best to make sure that other immune cells aren’t attacking undeserving human cells. When autoimmune diseases like asthma, allergies, or rheumatoid arthritis get out of control, there’s usually something wrong with the t-regs.

“We thought that this [variation in transcription factors] would be very rare, if it were found at all, in populations outside of rare disease families,” said Bulyk.

Since transcription factors are proteins, their existence depends on a DNA template, and transcription-factor-coding DNA is just as likely to develop mutations as any other gene. Most geneticists have more or less assumed that breaking a transcription factor would be very bad for an organism, because losing a transcription factor means several other genes will probably get thrown out of whack.

The deCODE project sequenced the complete genomes of 2,636 Icelanders and gathered partial genomes from tens of thousands more. It’s the largest population-level genome-data-gathering project to date. Almost 1 in 10 of the Icelanders studied (7.7%) had a “complete loss of function” mutation that would most likely completely break one of their genes.

And Bulyk’s team found that a lot of those non-disease-causing mutations were in transcription factors.[Correction:Their analysis had two parts: One where they combed through the other data sets and identified which transcription factors had the most mutant versions– as opposed to trancription factors that would be identical across 64,000 people. In the second part of their analysis, they compared their list of frequently-mutated transcription factors to the genes where the deCODE study identified a complete loss of function. “The transcription factors for which we found a larger number of damaging variants among 1kGP, ESP, and ExAC individuals, are more likely to be in TFs that are loss-of-function-tolerant,” Bulyk wrote in an email. Basically, mutations that change transcription factors’ ability to bind their target DNA pattern, seem to be pretty survive-able in some transcription factors. People with mutations in the most frequently-altered transcription factors were healthy enough to give informed consent and DNA samples. Which suggests that walking around with a gene expression mutation may not be super-unusual.]

Of course, it’s possible that some of the Icelanders were sick but undiagnosed or that others might have slight symptoms that are a bit too mild to register as disease. “Or maybe they just somehow contribute to making us different without being a disease,” Bullyk added.

Some transcription factors are not-negotiable. They have to be able to bind to a specific DNA sequence or else all hell breaks loose in a tissue. “There were these mutations known to cause human disease that land in transcription factors and impair their ability to recognize their target sites,” Bulyk said.

But other mutations may simply make transcription factors less efficient at the job. Or they may slightly alter the TF’s target, transforming a “CATGATTAT”-seeker into a “CATGATTTT”-seeker. A third possibility is that since transcription factors have overlapping jurisdictions–as in, many genes can be manipulated by several different TFs–one of the others may be picking up the slack.

Bottom-line: Mutations in transcription factors and the DNA base pairs where they like to land are common enough that every single human alive probably has their own, unique pattern of transcription factor behavior.

The fact that we all use our genes differently— even when compared to people with identical genes– isn’t breaking news to epigeneticists. But it does complicate attempts to predict disease based on genome sequence alone.

“A lot of people are starting to go out and get their genomes sequenced. And there are some studies where they’re finding undiagnosed diseases. And while the cost of genome sequencing has gone down, what remains a significant challenge now is genome interpretation,” said Bulyk (in a possible contender for “Scientist Understatement of the Decade”).

“It’s not as if you get a mutation and it either had no effect-meaning, it’s neutral– or there’s a complete loss of function.” she added. “There’s a wide spectrum of effects. Some are very subtle; some are very dramatic.”

In other words, genes are far from destiny. They’re part of a system with thousands of checks and counterbalances. TFs are just one class of genetic balancer.

**tl;dr:**

Your cells are teaming with little proteins that can bind to DNA and control how you use your genetic blueprints.

They’re called transcription factors and are pretty awesome.

]]>http://dianacrowscience.com/transcription-factors-the-listicle/feed/0418Splice of Life: 3 Examples of How Nature Edits Its Own Geneshttp://dianacrowscience.com/splice-up-yr-life/
http://dianacrowscience.com/splice-up-yr-life/#commentsFri, 29 Jan 2016 02:02:29 +0000http://dianacrowscience.com/?p=309About the “Under the Radar” series: Some scientific concepts come up again and again in interviews with scientists but never find their way into newspaper headlines. Each post in this series follows one of those biology “bogeys” that fly under journalism’s radar through 3 different mini-stories.

Story #1: Scientists splice up a CRISPR chicken…and find an evolutionary shortcut

Birds’ brains have all of the tools to make mammal-like neurons, according to a study in Science from August. And, incredibly, the researchers behind the study only had to tinker with one gene that changes how chicken cells edit their RNA to unlock several seemingly unrelated mammal neuron traits in chicken neural precursor cells.

It was as if the chicken cells instantly acquired a whole bunch of mutations at once, instead of just one.

Researchers think that this gene editing process– aka “alternative splicing”–may explain why some traits seem to have evolved at such high speeds.

“This is a process that has diverged very rapidly during evolution to produce different versions of proteins,” University of Toronto geneticist Ben Blencowe explained in a phone interview.

DNA cannot control an organism’s traits all by itself. For a gene to become a trait, the cell has to send an RNA copy of the gene to a tiny molecular factory called a ribosome. Ribosomes’ job is to build molecular machines called proteins. Proteins are the ones that run around the cell, doing all the little biochemical tasks that keep you alive, and they’re the ones that determine the final trait– usually (more on that in a later post).

Before an RNA leaves the nucleus, it has to get past little RNA editors called spliceosomes which cut unneeded base pairs out. Chickens’ spliceosomes are pretty similar to mammals’, but not identical. So when the researchers replaced one of the chicken cells’ RNA-editing genes with the mammalian version, they ended up with chicken “neural precursor” cells that build mammals’ neural proteins.

Blenclowe’s team concluded that switching up splicing patterns is big part of how animals keep up with rapidly changing evolutionary pressures, and his team isn’t the only one saying so. An MIT team lead by Christopher Burge came to the same conclusion based on a separate set of evidence. Burge’s team also pointed out that many of the genes that have alternative edits are also genes that play big roles in cancer.

Meet the Bogey: Alternative Splicing

Thanks to alternative splicing, most genes can code for more than one trait.That ability comes in handy when big, multicellular bodies need to make different kinds of cells. If one version of Protein A works best for neurons and another slightly different version of Protein A is best for muscle cells, then it’s helpful to have a single gene that can code for both. All you need is a tiny chemical cue that shows up in neurons but not muscles, and Presto! When the RNA-building and editing machinery sees that chemical, it’ll switch to making the neuron version.

If all of this is giving you a headache, trust me: you are not alone.

(The way I remember it is with a baking analogy: Say that you and your friend share a cookbook, but when you make chocolate chip cookies, you like to swap out the chocolate chips with M&Ms. If one of your friends is a stickler for following the recipe exactly, their chocolate chip cookies will turn out pretty similar to your M&M cookies but there will be slight differences.

Same principle with alternative edits of the same gene: The differences in the final protein or trait are usually pretty small, but they can change behavior or traits. Also, while some alternative splicing is accidental– like leaving out the salt–many splicing variants are actually deliberate and beneficial– like using M&Ms instead of chocolate chips.)

At the turn of the millennium, most geneticists thought that only 6% of genes had useful alternate edits– aka “splicing isoforms“– but as it became easier and easier to sequence genomes and track RNAs, the number of genes known to have splicing isoforms skyrocketed. “Now we know that it’s 90% or more [of all genes],” UCSD computer scientist Christian Barrett told me during a phone interview.

Any process that occurs that frequently in living cells has to be useful, but figuring out how to crunch the data we have on splicing isoforms and convert it into medically useful information is proving to be a daunting task…

The human genome has about about 20,000 genes, but those 20,000 genes can make hundreds of thousands of different proteins. There are about 300,000 known (or at least, genomics’ most reliable computer programs say there are 300,000) protein isoforms in human cells. In other words, there’s evidence that alternative splicing produces an average of 15 different proteins for every individual gene.

Developing a computer program that could glean that useful cancer-identifying information from a sea of hundreds of thousands of RNA transcripts took Frazer and Barrett’s team about five years. And in the process, they realized that the previous estimate of total human splicing isoform products was actually probably too low. Based on the data they were seeing in ovarian cells, the total number could be closer to 400,000 or even 600,000.

“I think at lot of people would have just given up give how complex it was to design this experiment,” Frazer said.

Still, she’s optimistic that using computers to sift through RNA transcripts could lead to more accurate diagnoses. Her team is currently doing an exploratory trial to see whether the RNAs their software highlighted are present in cells from women who are currently receiving treatment for ovarian cancer.

If all goes well, they may be able to develop a simple test where doctors can take a few cells from a pap smear sample and check to see if there are any cancer-correlated RNAs in them. A test like that wouldn’t be a silver bullet, but it would probably help doctors catch ovarian cancers earlier.

Story #3: Can’t sleep? Alternative splicing might be partly to blame.

Foster and Pierson are neuroscientists, not geneticists, so they measure the protein’s effects by recording how often melanopsin-expressing neurons fire and how long each of those neuron firings lasts. Most neuron-controlling proteins cause neurons to fire in one, more-or-less predictable pattern. But when they tested melanopsin, they consistently saw two distinct neuron firing patterns.

“We were getting two messages and two proteins and thought ‘What the HELL is going on here?!'” said Foster.

Geneticists know enough about splicing to predict which portions of genes are most likely to be edited out, so when Foster and Pierson asked a geneticist colleague to take a look at melanopsin’s DNA template, they were able to ID a section in the melanopsin gene that looked highly spliceable. That meant that most lab mice probably had both a “long-tail” version of melanopsin and a “short-tail” version in their retinal cells.

The mice without short-tail melanopsin couldn’t shrink their pupils in response to bright light. However, they still responded to light the way most respectable nocturnal lab mice do: by slowing down and acting sleepy.

In contrast, the mice without the long-tail melanopsin could adjust their pupils to the light, but the light didn’t make them sleepy. Instead, they more or less behaved like tiny rodent insomniacs. Foster compared their lack of circadian rhythm to a case of neverending jetlag.

So the group’s next question is: What do melanopsins do in humans?

The human version of the melanopsin gene is pretty similar to the mouse one in terms of DNA base pairs, and it has the potential to be spliced into long-tail and short-tail versions. It seems plausible that human long-tailed melanopsin could help us adjust our pupils, but since we’re active during the day, all bets are off when it comes to what the human short-tailed melanopsin might do.

Humans actually exhibit the inverse of the mouse response to bright light; we get sleepy and sluggish when lights go dim. Foster says that if you were one of those people who drifted off to sleep during dimly lit lectures in college, “Not all of that would be the fault of your lecturer.”

So even though it’s kind of tempting to speculate that a splicing isoform controlling our response to dimly lit classrooms might be partly responsible for why so many people forget about RNA after they’re out of school, at this point, we really don’t know.

There are obvious ethical problems with knocking out protein isoforms in human subjects, especially when there’s reason to think doing so might put them at risk of insomnia.

Foster and Pierson are, however, on the lookout for humans who may have natural mutations affecting their melanopsin splices. However, only time will tell if they’re able to find someone with an identifiable melanopsin mutation.

Still, their study is one of the first to show a single splicing event creating two proteins that control two different behaviors. It probably won’t be the last…

tl;dr:

Cells can build several different things from just one gene. This makes sorting out which gene causes which trait a lot more complicated.